[Bioc-devel] deprecated extractTranscriptsFromGenome

James W. MacDonald jmacdon at uw.edu
Mon Mar 10 17:04:02 CET 2014

Hi Raf,

Under ?extractTranscriptsFromGenome I see this:


WARNING: The tools described in this man page are obsolete and in
the process of being DEPRECATED.

‘extractTranscriptsFromGenome’ extracts the transcript sequences
from a BSgenome data package using the transcript information
(exon boundaries) stored in a TranscriptDb or GRangesList object.
DEPRECATED. Please use ‘extractTranscriptSeqs’ instead.

‘extractTranscripts’ extracts a set of transcripts from a single
DNA sequence. DEPRECATED. Please use ‘extractTranscriptSeqs’

Related utilities:

‘transcriptWidths’ to get the lengths of the transcripts (called
the "widths" in this context) based on the boundaries of their

‘transcriptLocs2refLocs’ converts transcript-based locations into
reference-based (aka chromosome-based or genomic) locations.

‘sortExonsByRank’ orders (or reorders) by rank the exons stored in
a GRangesList object containing exons grouped by transcript.



On 3/10/2014 11:57 AM, rcaloger wrote:
> Hi, I am the maintainer of chimera package
> I got an warning indicating the extractTranscriptsFromGenome and
> extractTranscripts functions from GenomicFeatures package are deprecated.
> Does anybody could tell me which are the functions that are going to
> substitute them?
> Cheers
> Raf

James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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